Steps to Manually Fix:
I was able to fix the warnings by:
1) From database, get content of exp_sites > site_pages
2) Deserialize
3) Remove all references to entry_id in deserialized array.
4) Serialize and base64 encode.
5) Move serialized data back to exp_sites > site_pages.

I’m not able to replicate it in the latest 3.5.11. I do see a bug fix in 3.5.8 that looks like it might apply:

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